W1: Introduction to R
author: Ania Majewska and Reni Kaul date: May 22, 2019 autosize: true font-import: https://fonts.googleapis.com/css?family=PT+Sans font-family: ‘PT Sans’, sans-serif;
Why is R programming a useful skill?
About today’s instructors
Ania Majewska - My research interest is in conservation biology and disease ecology - I use R in my research to: + organize and wrangle data + analyze data (statistical models) + model disease dynamics (transmission) - I mostly work on the monarch butterfly and it’s protozoan parasite - My contact info is majewska@uga.edu
About today’s instructors
Reni Kaul - My research interest is [INSERT DESCRIPTION] - I use R in my research to: + organize data + develop machine learning algorithms + [INSERT DETAILS] - I mostly work [in this disease system or approach] - My contact info is [INSERT EMAIL]
Workshop Goals
left:65% The workshop series consists of four half day workshops each focusing on a different part of the research process - Introduction to R (Today: Ania Majewska and Reni Kaul) - Reproducible research (May 29; Deven Vishwas Gokhale and Reni Kaul ) - Simulating infectious diseases (June 3; John Vinson) - Visualizing data (June 7; Robbie Richards)
workflow
Workshop Format
- Introduction of instructor & how they use
R - Review of past concepts
- Outline of the day’s goals
- Work through data analysis project
- Reflection on day’s materials
Expectations
left:60% You - Come ready to participate + do the reading + review the materials beforehand - Ask questions - Help each other
Instructors - Come prepared - Help you find answers - Be a resource for you during the REU program
Outline
left: 40%
At the end of this workshop you should be able to… - calculate summary statistics of a dataset - create a figure from data
Today
Topics 1. What is R and RStudio? 2. Introduction to R and tidyverse
Break 3. Code along / Exercise
Break 4. Troubleshooting
5. Exploring data in groups
Break 6. Wrap Up 7. Datacamp.com
1. What is R and RStudio?
left: 50%
- free, open source programming language with a pre-set functionality (base
R) - Functionality is extented by
Rpackages which are collections of functions and data sets developed by the community.
- RStudio is a software program that makes
Rprogramming easier: - write and test code efficiently
- organizing files into projects
- intergrating other programming lanuguages (e.g., Latex)
RStudio
Let’s open Rstudio!
RStudio
RStudio
2. Introduction to tidyverse
left: 50%
- The tidyverse is a set of packages that work in harmony because they share common design.
- Unique syntax used pipes (
%>%) to connect data (object) to verbs (functions).
tidy syntax
tidyverse package
The tidyverse package is designed to make it easy to install and load core packages from the tidyverse in a single command.
tidy verse package
Install tidyverse package
- We need to install the
tidyversepackage. This can be done by clicking on buttons in Rstudio or from the console usinginstall.packages() - Install the package by running the line
# install all the packages in the tidyverse
install.packages("tidyverse") Load tidyverse package
- Once a package is installed, we need to load it during our current R session.
- This is done using
library().
# load tidyverse library
library(tidyverse)========================================================
Download the W1_Exercise zip file
Unzip and open the folder.
Open W1_Exercise.Rproj
========================================================
Break
Resume in 15 min========================================================
Open W1_Exercise.Rmd
How to get unstuck: functions
left: 35% - Every function has a help page - ?function() to access
manual page
How to get unstuck: packages
left: 50% * Packages have a vignette and/or reference manual on cran.r-project.org
- People often make their own tutorials too ***
How to get unstuck: packages
left: 30%
- Cheatsheets published by RStudio
cheatsheets
How to get unstuck: packages
left: 30%
- Cheatsheets published out by RStudio
- Contributed cheatsheets
cheatsheets
How to get unstuck: error messages
error
First, try to understand the error message. It can be very helpful.
How to get unstuck: error messages
left: 30%
- But sometimes, the messages is cryptic. So use google!
Exploring further
Let’s work in small groups (max of 3)
- Develop a question that can be answered with this data
- Decide on the needed verbs, and order
- Write the code in the final code chunck of the
W1_Exercise.Rmdfile
More instructions in the file.
Wrap Up
left: 50%
We can… - calculate summary statistics of a dataset - create a figure from data
using - dplyr package - filter, arrange… - ggplot2 package - geom_point, facet…
W1
Wrap Up
left: 50%
Next week
Focus on communication by following best practices for reproducible research
W1
Datacamp.com
We will be using datacamp.com to build more skills!